BeviMed (version 1.2)

probability_pathogenic: Calculate region or variant-level probability of pathogencity given prior probability on pathogenicity of region

Description

Calculate region or variant-level probability of pathogencity given prior probability on pathogenicity of region

Usage

probability_pathogenic(prior = 0.05, variant_level = FALSE, y, G,
  min_ac = 1, ...)

Arguments

prior

Numeric value giving prior for probability of pathogenicity of region.

variant_level

Logical value determining whether to return the probabilities of pathogenicity for the individual variants or for the region as a whole.

y

Logical vector of case (TRUE) control (FALSE) status.

G

Integer matrix of variant counts per individual, one column per individual and one row per variant.

min_ac

Minimum allele count per individual to be considered to have a pathogenic combination of variants. '1' could correspond to a dominant inheritance hypothesis whereas '2' could correspond to a recessive inheritance hypothesis.

...

Other arguments to pass to bevimed.

Value

• Probabilities of pathogenicity.